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Goniodysgenesis is a developmental abnormality of the anterior chamber of the eye. It is generally considered to be congenital in dogs (Canis lupus familiaris), and has been associated with glaucoma and blindness. Goniodysgenesis and early-onset glaucoma initially emerged in Border Collies in Australia in the late 1990s and has subsequently been found in Europe and the USA. The objective of the present study was to determine the genetic basis of goniodysgenesis in Border Collies. Clinical diagnosis was based on results of examinations by veterinary ophthalmologists of affected and unaffected dogs from eleven different countries. Genotyping using the Illumina high density canine SNP chip and whole genome sequencing were used to identify candidate genetic regions. Expression profiles and evolutionary conservation of candidate genes were assessed using public databases. Analysis of pedigree information was consistent with an autosomal recessive mode of inheritance for severe goniodysgenesis (potentially leading to glaucoma) in this breed. There was a highly significant peak of association over chromosome 17, with a p-value of 2 × 10-13. Whole genome sequences of three dogs with glaucoma, three severely affected and three unaffected dogs identified a missense variant in the olfactomedin like 3 (OLFML3) gene in all six affected animals. This was homozygous in all nine cases with glaucoma and 12 of 14 other severely affected animals. Of 67 reportedly unaffected animals, only one (offspring of two homozygous affected parents) was homozygous for this variant. The identification of a candidate genetic region and putative causative mutation will aid breeders to reduce the frequency of goniodysgenesis and the risk of glaucoma in the Border Collie population.

The western subspecies of Yellow-billed Cuckoo Coccyzus americanus occidentalis has undergone severe population declines over the last two decades. Numerous petitions have warranted its listing under the Endangered Species Act; however, the question of whether the western subspecies is genetically separated from the eastern C. a. americanus form is controversial. Previous research found small, but significant divergence in a single mitochondrial gene based on a limited number of samples. In this study, I analyze 949 base pairs of the same mitochondrial cytochrome b gene from additional samples in both the western and eastern subspecies to reassess the evolutionary distinctiveness of the western taxa. Unlike the previous study, I did not find any fixed genetic differences, but only found slight, insignificant genetic differentiation between the subspecies. The separation into distinct subspecies of the eastern and western Yellow-billed Cuckoo might be more recent than can be captured by a single mitochondrial gene; alternatively high levels of gene flow might prevent complete segregation. Interestingly, I found a substantial amount of haplotype variation within the western samples, which may indicate genetic differences between western sampling locations. Future studies incorporating next generation sequencing are recommended to resolve the taxonomic status of Yellow-billed Cuckoo.

We identified 247 unique ruff (Philomachus pugnax) microsatellite sequences. Primer sets were designed from 102 selected loci and tested in 12–24 individuals from a captive population. Sequence homology was used to assign locations in the chicken (Gallus gallus) and/or zebra finch (Taeniopygia guttata) genome for the majority of these loci. Fifty-two loci were found to be polymorphic and 47 of these were typed in known families. Forty-six loci displayed Mendelian inheritance including Ppu058, which was confirmed to be Z-linked by the complete absence of any heterozygous females.

Three strikingly different alternative male mating morphs (aggressive 'independents', semicooperative 'satellites' and female-mimic 'faeders') coexist as a balanced polymorphism in the ruff, Philomachus pugnax, a lek-breeding wading bird(1-3). Major differences in body size, ornamentation, and aggressive and mating behaviors are inherited as an autosomal polymorphism(4,5). We show that development into satellites and faeders is determined by a supergene(6-8) consisting of divergent alternative, dominant and non-recombining haplotypes of an inversion on chromosome 11, which contains 125 predicted genes. Independents are homozygous for the ancestral sequence. One breakpoint of the inversion disrupts the essential CENP-N gene (encoding centromere protein N), and pedigree analysis confirms the lethality of homozygosity for the inversion. We describe new differences in behavior, testis size and steroid metabolism among morphs and identify polymorphic genes within the inversion that are likely to contribute to the differences among morphs in reproductive traits.

Sequence variation in the melanocortin-1 receptor (MC1R) gene explains color morph variation in several species of birds and mammals. Ruffs (Philomachus pugnax) exhibit major dark/light color differences in melanin-based male breeding plumage which is closely associated with alternative reproductive behavior. A previous study identified a microsatellite marker (Ppu020) near the MC1R locus associated with the presence/absence of ornamental plumage. We investigated whether coding sequence variation in the MC1R gene explains major dark/light plumage color variation and/or the presence/absence of ornamental plumage in ruffs. Among 821bp of the MC1R coding region from 44 male ruffs we found 3 single nucleotide polymorphisms, representing 1 nonsynonymous and 2 synonymous amino acid substitutions. None were associated with major dark/light color differences or the presence/absence of ornamental plumage. At all amino acid sites known to be functionally important in other avian species with dark/light plumage color variation, ruffs were either monomorphic or the shared polymorphism did not coincide with color morph. Neither ornamental plumage color differences nor the presence/absence of ornamental plumage in ruffs are likely to be caused entirely by amino acid variation within the coding regions of the MC1R locus. Regulatory elements and structural variation at other loci may be involved in melanin expression and contribute to the extreme plumage polymorphism observed in this species.

Maintaining polymorphisms for genes with effects of ecological significance may involve conflicting selection in males and females. We present data from a captive population of ruffs (Philomachus pugnax) showing that a dominant allele controls development into both small, ‘female mimic’ males (‘faeders’), and a previously undescribed class of small ‘female faeders’. Most male ruffs have elaborate breeding plumage and display behaviour, but 0.5–1.5% are faeders, which lack both. Females from a captive population previously lacking faeders were bred with two founder faeder males and their faeder sons. The faeders’ offspring had a quadrimodal size distribution comprising normal-sized males and females, faeders and atypically small females. By contrast, ornamented males fathered only normal-sized offspring. We conclude that both founding faeders were heterozygous for a faeder allele absent from the original population. This allele is dominant to previously described genes that determine development into independent versus satellite ornamented males. Unlike those genes, the faeder allele is clearly expressed in females. Small body size is a component of the male faeder mating strategy, but provides no obvious benefit to females. Bisexual expression of the gene provides the opportunity to quantify the strength of sexually antagonistic selection on a Mendelian trait.

A linkage map of the ruff (Philomachus pugnax) genome was constructed based on segregation analysis of 58 microsatellite loci from 381 captive-bred individuals spanning fourteen breeding years and comprising 64 families. Twenty-eight of the markers were resolved into seven linkage groups and five single marker loci, homologous to known chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) chromosomes. Linkage groups range from 10.1 to 488.7 cM in length and covered a total map distance of 641.6 cM, corresponding to an estimated 30–35% coverage of the ruff genome, with a mean spacing of 22.9 cM between loci. Through comparative mapping, we are able to assign linkage groups Ppu1, Ppu2, Ppu6, Ppu7, Ppu10, Ppu13, and PpuZ to chromosomes and identify several intrachromosomal rearrangements between the homologs of chicken, zebra finch, and ruff microsatellite loci. This is the first linkage map created in the ruff and is a major step toward providing genomic resources for this enigmatic species. It will provide an essential framework for mapping of phenotypically and behaviorally important loci in the ruff.

By next generation transcriptome sequencing, it is possible to obtain data on both nucleotide sequence variation and gene expression. We have used this approach (RNA-Seq) to investigate the genetic basis for differences in plumage coloration and mating strategies in a non-model bird species, the ruff (Philomachus pugnax). Ruff males show enormous variation in the coloration of ornamental feathers, used for individual recognition. This polymorphism is linked to reproductive strategies, with dark males (Independents) defending territories on leks against other Independents, whereas white morphs (Satellites) co-occupy Independent's courts without agonistic interactions. Previous work found a strong genetic component for mating strategy, but the genes involved were not identified. We present feather transcriptome data of more than 6,000 de-novo sequenced ruff genes (although with limited coverage for many of them). None of the identified genes showed significant expression divergence between males, but many genetic markers showed nucleotide differentiation between different color morphs and mating strategies. These include several feather keratin genes, splicing factors, and the Xg blood-group gene. Many of the genes with significant genetic structure between mating strategies have not yet been annotated and their functions remain to be elucidated. We also conducted in-depth investigations of 28 pre-identified coloration candidate genes. Two of these (EDNRB and TYR) were specifically expressed in black- and rust-colored males, respectively. We have demonstrated the utility of next generation transcriptome sequencing for identifying and genotyping large number of genetic markers in a non-model species without previous genomic resources, and highlight the potential of this approach for addressing the genetic basis of ecologically important variation.

The issue of inherited disorders and poor health in pedigree dogs has been widely discussed in recent years. With the advent of genome-wide sequencing technologies and the increasing development of new diagnostic DNA disease tests, the full extent and prevalence of inherited disorders in pedigree dogs is now being realized. In this review we discuss the challenges facing pedigree dog breeds: the common pitfalls and problems associated with combating single gene mediated disorders, phenotypic selection on complex disorders, and ways of managing genetic diversity. Breeding strategies incorporating screening schemes have been shown to be successful in significantly reducing the prevalence of an inherited disorder and improving the overall health in certain breeds. However, with 215 breeds officially recognized by the Kennel Club in the United Kingdom and 396 inherited disorders currently identified, many breeds have reached the point at which successfully breeding away from susceptible individuals at a population-wide scale will require new genomic selection strategies in combination with currently available breeding schemes. Whilst DNA-based tests identifying disease causing mutation(s) remain the most informative and effective approach for single gene disorder disease management, they must be used along with current screening schemes, genomic selection, and pedigree information in breeding programs in the effort to maintain genetic diversity while also significantly reducing the number of inherited disorders in pedigree dogs. Electronic supplementary material The online version of this article (doi:10.1186/s40575-015-0014-9) contains supplementary material, which is available to authorized users.